I was invited to speak about "Citizen Microbiology" at the Lake Arrowhead Microbial Genomics meeting on (my birthday!) September 16th, 2014.
I decided to focus on two of the challenges associated with Citizen Microbiology: 1) the fact that microbes are invisible, and 2) the fact that the current tools for visualization of complex microbial community data are not ideal.
I present Winogradsky columns as a way to engage the public with microbial communities, particularly in a classroom setting. I also present the human face as a visualization tool for complex microbial community data.
Many people strive to attain lighter, brighter, healthier-looking skin. Learning to properly care for your skin on a day-to-day basis will help your skin stay light and tight, while more substantial and scientifically-proven lightening products are also widely available.
A donkey's your uncle and a roundworm's your cousin! That's not entirely true, but you might be surprised by just how closely related you are.
Register to explore the whole course here: https://school.bighistoryproject.com/bhplive?WT.mc_id=Slideshare12202017
Many people strive to attain lighter, brighter, healthier-looking skin. Learning to properly care for your skin on a day-to-day basis will help your skin stay light and tight, while more substantial and scientifically-proven lightening products are also widely available.
A donkey's your uncle and a roundworm's your cousin! That's not entirely true, but you might be surprised by just how closely related you are.
Register to explore the whole course here: https://school.bighistoryproject.com/bhplive?WT.mc_id=Slideshare12202017
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
ISI 2024: Application Form (Extended), Exam Date (Out), EligibilitySciAstra
The Indian Statistical Institute (ISI) has extended its application deadline for 2024 admissions to April 2. Known for its excellence in statistics and related fields, ISI offers a range of programs from Bachelor's to Junior Research Fellowships. The admission test is scheduled for May 12, 2024. Eligibility varies by program, generally requiring a background in Mathematics and English for undergraduate courses and specific degrees for postgraduate and research positions. Application fees are ₹1500 for male general category applicants and ₹1000 for females. Applications are open to Indian and OCI candidates.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
2024 State of Marketing Report – by HubspotMarius Sescu
https://www.hubspot.com/state-of-marketing
· Scaling relationships and proving ROI
· Social media is the place for search, sales, and service
· Authentic influencer partnerships fuel brand growth
· The strongest connections happen via call, click, chat, and camera.
· Time saved with AI leads to more creative work
· Seeking: A single source of truth
· TLDR; Get on social, try AI, and align your systems.
· More human marketing, powered by robots
ChatGPT is a revolutionary addition to the world since its introduction in 2022. A big shift in the sector of information gathering and processing happened because of this chatbot. What is the story of ChatGPT? How is the bot responding to prompts and generating contents? Swipe through these slides prepared by Expeed Software, a web development company regarding the development and technical intricacies of ChatGPT!
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
ISI 2024: Application Form (Extended), Exam Date (Out), EligibilitySciAstra
The Indian Statistical Institute (ISI) has extended its application deadline for 2024 admissions to April 2. Known for its excellence in statistics and related fields, ISI offers a range of programs from Bachelor's to Junior Research Fellowships. The admission test is scheduled for May 12, 2024. Eligibility varies by program, generally requiring a background in Mathematics and English for undergraduate courses and specific degrees for postgraduate and research positions. Application fees are ₹1500 for male general category applicants and ₹1000 for females. Applications are open to Indian and OCI candidates.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
2024 State of Marketing Report – by HubspotMarius Sescu
https://www.hubspot.com/state-of-marketing
· Scaling relationships and proving ROI
· Social media is the place for search, sales, and service
· Authentic influencer partnerships fuel brand growth
· The strongest connections happen via call, click, chat, and camera.
· Time saved with AI leads to more creative work
· Seeking: A single source of truth
· TLDR; Get on social, try AI, and align your systems.
· More human marketing, powered by robots
ChatGPT is a revolutionary addition to the world since its introduction in 2022. A big shift in the sector of information gathering and processing happened because of this chatbot. What is the story of ChatGPT? How is the bot responding to prompts and generating contents? Swipe through these slides prepared by Expeed Software, a web development company regarding the development and technical intricacies of ChatGPT!
Product Design Trends in 2024 | Teenage EngineeringsPixeldarts
The realm of product design is a constantly changing environment where technology and style intersect. Every year introduces fresh challenges and exciting trends that mold the future of this captivating art form. In this piece, we delve into the significant trends set to influence the look and functionality of product design in the year 2024.
How Race, Age and Gender Shape Attitudes Towards Mental HealthThinkNow
Mental health has been in the news quite a bit lately. Dozens of U.S. states are currently suing Meta for contributing to the youth mental health crisis by inserting addictive features into their products, while the U.S. Surgeon General is touring the nation to bring awareness to the growing epidemic of loneliness and isolation. The country has endured periods of low national morale, such as in the 1970s when high inflation and the energy crisis worsened public sentiment following the Vietnam War. The current mood, however, feels different. Gallup recently reported that national mental health is at an all-time low, with few bright spots to lift spirits.
To better understand how Americans are feeling and their attitudes towards mental health in general, ThinkNow conducted a nationally representative quantitative survey of 1,500 respondents and found some interesting differences among ethnic, age and gender groups.
Technology
For example, 52% agree that technology and social media have a negative impact on mental health, but when broken out by race, 61% of Whites felt technology had a negative effect, and only 48% of Hispanics thought it did.
While technology has helped us keep in touch with friends and family in faraway places, it appears to have degraded our ability to connect in person. Staying connected online is a double-edged sword since the same news feed that brings us pictures of the grandkids and fluffy kittens also feeds us news about the wars in Israel and Ukraine, the dysfunction in Washington, the latest mass shooting and the climate crisis.
Hispanics may have a built-in defense against the isolation technology breeds, owing to their large, multigenerational households, strong social support systems, and tendency to use social media to stay connected with relatives abroad.
Age and Gender
When asked how individuals rate their mental health, men rate it higher than women by 11 percentage points, and Baby Boomers rank it highest at 83%, saying it’s good or excellent vs. 57% of Gen Z saying the same.
Gen Z spends the most amount of time on social media, so the notion that social media negatively affects mental health appears to be correlated. Unfortunately, Gen Z is also the generation that’s least comfortable discussing mental health concerns with healthcare professionals. Only 40% of them state they’re comfortable discussing their issues with a professional compared to 60% of Millennials and 65% of Boomers.
Race Affects Attitudes
As seen in previous research conducted by ThinkNow, Asian Americans lag other groups when it comes to awareness of mental health issues. Twenty-four percent of Asian Americans believe that having a mental health issue is a sign of weakness compared to the 16% average for all groups. Asians are also considerably less likely to be aware of mental health services in their communities (42% vs. 55%) and most likely to seek out information on social media (51% vs. 35%).
AI Trends in Creative Operations 2024 by Artwork Flow.pdfmarketingartwork
This article is all about what AI trends will emerge in the field of creative operations in 2024. All the marketers and brand builders should be aware of these trends for their further use and save themselves some time!
A report by thenetworkone and Kurio.
The contributing experts and agencies are (in an alphabetical order): Sylwia Rytel, Social Media Supervisor, 180heartbeats + JUNG v MATT (PL), Sharlene Jenner, Vice President - Director of Engagement Strategy, Abelson Taylor (USA), Alex Casanovas, Digital Director, Atrevia (ES), Dora Beilin, Senior Social Strategist, Barrett Hoffher (USA), Min Seo, Campaign Director, Brand New Agency (KR), Deshé M. Gully, Associate Strategist, Day One Agency (USA), Francesca Trevisan, Strategist, Different (IT), Trevor Crossman, CX and Digital Transformation Director; Olivia Hussey, Strategic Planner; Simi Srinarula, Social Media Manager, The Hallway (AUS), James Hebbert, Managing Director, Hylink (CN / UK), Mundy Álvarez, Planning Director; Pedro Rojas, Social Media Manager; Pancho González, CCO, Inbrax (CH), Oana Oprea, Head of Digital Planning, Jam Session Agency (RO), Amy Bottrill, Social Account Director, Launch (UK), Gaby Arriaga, Founder, Leonardo1452 (MX), Shantesh S Row, Creative Director, Liwa (UAE), Rajesh Mehta, Chief Strategy Officer; Dhruv Gaur, Digital Planning Lead; Leonie Mergulhao, Account Supervisor - Social Media & PR, Medulla (IN), Aurelija Plioplytė, Head of Digital & Social, Not Perfect (LI), Daiana Khaidargaliyeva, Account Manager, Osaka Labs (UK / USA), Stefanie Söhnchen, Vice President Digital, PIABO Communications (DE), Elisabeth Winiartati, Managing Consultant, Head of Global Integrated Communications; Lydia Aprina, Account Manager, Integrated Marketing and Communications; Nita Prabowo, Account Manager, Integrated Marketing and Communications; Okhi, Web Developer, PNTR Group (ID), Kei Obusan, Insights Director; Daffi Ranandi, Insights Manager, Radarr (SG), Gautam Reghunath, Co-founder & CEO, Talented (IN), Donagh Humphreys, Head of Social and Digital Innovation, THINKHOUSE (IRE), Sarah Yim, Strategy Director, Zulu Alpha Kilo (CA).
Trends In Paid Search: Navigating The Digital Landscape In 2024Search Engine Journal
The search marketing landscape is evolving rapidly with new technologies, and professionals, like you, rely on innovative paid search strategies to meet changing demands.
It’s important that you’re ready to implement new strategies in 2024.
Check this out and learn the top trends in paid search advertising that are expected to gain traction, so you can drive higher ROI more efficiently in 2024.
You’ll learn:
- The latest trends in AI and automation, and what this means for an evolving paid search ecosystem.
- New developments in privacy and data regulation.
- Emerging ad formats that are expected to make an impact next year.
Watch Sreekant Lanka from iQuanti and Irina Klein from OneMain Financial as they dive into the future of paid search and explore the trends, strategies, and technologies that will shape the search marketing landscape.
If you’re looking to assess your paid search strategy and design an industry-aligned plan for 2024, then this webinar is for you.
5 Public speaking tips from TED - Visualized summarySpeakerHub
From their humble beginnings in 1984, TED has grown into the world’s most powerful amplifier for speakers and thought-leaders to share their ideas. They have over 2,400 filmed talks (not including the 30,000+ TEDx videos) freely available online, and have hosted over 17,500 events around the world.
With over one billion views in a year, it’s no wonder that so many speakers are looking to TED for ideas on how to share their message more effectively.
The article “5 Public-Speaking Tips TED Gives Its Speakers”, by Carmine Gallo for Forbes, gives speakers five practical ways to connect with their audience, and effectively share their ideas on stage.
Whether you are gearing up to get on a TED stage yourself, or just want to master the skills that so many of their speakers possess, these tips and quotes from Chris Anderson, the TED Talks Curator, will encourage you to make the most impactful impression on your audience.
See the full article and more summaries like this on SpeakerHub here: https://speakerhub.com/blog/5-presentation-tips-ted-gives-its-speakers
See the original article on Forbes here:
http://www.forbes.com/forbes/welcome/?toURL=http://www.forbes.com/sites/carminegallo/2016/05/06/5-public-speaking-tips-ted-gives-its-speakers/&refURL=&referrer=#5c07a8221d9b
ChatGPT and the Future of Work - Clark Boyd Clark Boyd
Everyone is in agreement that ChatGPT (and other generative AI tools) will shape the future of work. Yet there is little consensus on exactly how, when, and to what extent this technology will change our world.
Businesses that extract maximum value from ChatGPT will use it as a collaborative tool for everything from brainstorming to technical maintenance.
For individuals, now is the time to pinpoint the skills the future professional will need to thrive in the AI age.
Check out this presentation to understand what ChatGPT is, how it will shape the future of work, and how you can prepare to take advantage.
A brief introduction to DataScience with explaining of the concepts, algorithms, machine learning, supervised and unsupervised learning, clustering, statistics, data preprocessing, real-world applications etc.
It's part of a Data Science Corner Campaign where I will be discussing the fundamentals of DataScience, AIML, Statistics etc.
Time Management & Productivity - Best PracticesVit Horky
Here's my presentation on by proven best practices how to manage your work time effectively and how to improve your productivity. It includes practical tips and how to use tools such as Slack, Google Apps, Hubspot, Google Calendar, Gmail and others.
The six step guide to practical project managementMindGenius
The six step guide to practical project management
If you think managing projects is too difficult, think again.
We’ve stripped back project management processes to the
basics – to make it quicker and easier, without sacrificing
the vital ingredients for success.
“If you’re looking for some real-world guidance, then The Six Step Guide to Practical Project Management will help.”
Dr Andrew Makar, Tactical Project Management
25. 0% 20% 40% 60% 80% 100%
Water 3
Water 2
Water 1
W Sediment
G Sediment
Y Sediment
Thaumarchaeota
Gammaproteobacteria
Alphaproteobacteria
Flavobacteriia
Deltaproteobacteria
Bacteroidia
Planctomycetia
Anaerolineae
26.
27. Eyebrows Alphaproteobacteria
Left Eye Anaerolinea
Right Eye Planctomycetia
Nose Flavobacteria
Left Ear Deltaproteobacteria
Right Ear Thaumarchaeota
Mouth Bacteroidia
Jawbone Gammaproteobacteria
28. Eyebrows Alphaproteobacteria
Left Eye Anaerolinea
Right Eye Planctomycetia
Nose Flavobacteria
Left Ear Deltaproteobacteria
Right Ear Thaumarchaeota
Mouth Bacteroidia
Jawbone Gammaproteobacteria
33. …said no one, ever.
“Now, THAT’S a good looking pie chart!”
“OMG, I know I’ve seen that pie chart somewhere before.”
Your pie chart looks exactly like a pie chart I knew in undergrad.”
“I can definitely see your dad’s pie chart in your pie chart.”
“When your pie chart was younger, it looked like your mom’s pie chart but now,
it’s looking more and more like your dad’s every day.”
“Wait a minute… your pie chart looks different.
Did you have something removed from it?”
Citizen science is scientific research conducted, in whole or in part, by amateur or nonprofessional scientists
Citizen science is not a new phenomenon. The Christmas Bird count is one of the oldest, running for over 100 years.
Not only was Darwin a citizen scientist himself, but he ran his own crowdsourced research, writing thousands of letters to naturalists around the world, asking them to share their observations with him.
So, why is there such a surge of interest in citizen science?
Not only is there a surge of general interest in Citizen Science, but the contribution of citizen science to the literature is on the rise.
A small minority of these publications are projects involving microbes. Why is that? With the stupid cheap and high-throughput sequencing that’s available, why is citizen microbiology not keeping up with the pace of sequence-enabled microbial ecology?
One answer might be that the public harbors misconceptions about microbes.
I like to use the google search autocomplete feature to gauge public interest and opinion on a subject, and as you can see, the public appears to actually be receptive to microbes, this is especially striking when we compare to more a charismatic species
I have firsthand experience of the general public’s willingness to engage with the microbial world around them.
Swab surfaces for growth competition
Swab cell phones and shoes
Swab the ISS
www.spacemicrobes.org
Microbial citizen science projects do suffer from unique challenges relative to other citizen science projects
I’m going to focus on two of them, what I will term the “invisibility problem” and the “pie chart problem”. Actually, after being told I sounded too negative, I’ll call them opportunities.
First, I’ll tackle the invisibility problem. As Noah mentioned yesterday, engaging people with organisms they cannot see can be a challenging task.
But, as many of you well know, microbes are not always invisible.
Many microbes are NOT invisible. In fact, they can be quite beautiful. If you carefully pry up a hunk of aquatic sediments, this is what you might find. These beautiful, colorful layers, each of which represents a different “ecotype” of microbe. This particular chunk is from the Great Sippewisset Salt Marsh. Some of you may be familiar with this place near the Marine Biological Laboratory in Woods Hole, Mass.
These layers form along sulfur and oxygen gradients that are created my microbial metabolic processes. And these layers are easy to replicate in the lab. You just mix some aquatic sediment with a carbon and sulfur source, usually shredded newspaper and egg yolks, top it off with water, seal it and forget it
It is a long-time dream of mine to use Winogradsky columns in my research, but I haven’t been motivated enough to seek funding to do so, and not clever enough to work them into my current research.
Until now…
Our lab is currently ramping up a seagrass microbiome project, one aspect of which is to better understand the plant-microbe interactions that are taking place in the rhizosphere. Both because we want reference genomes to enable better metagenomics and because we would eventually like to have isolates with which to do experiments, we are starting to think about how to culture the microbes that may play a key role in things like sulfur oxidation or nitrogen fixation in seagrass beds.
Rather than setting up culture conditions for a wide variety of organisms, some of which are quite fastidious, we are using Winogradsky columns to do some enrichments.
Here are some examples of winogradsky columns that we have growing in the lab right now. They’ve actually survived the flight here, and I’ll pass them around now so you can take a look at them.
2, 4, and 7 weeks post-inoculation
Recipe (with diatomaceous earth) 1g each cellulose and sodium sulfate, 0.1 g each ammonium chloride, calcium carbonate, and dibasic potassium phosphate
Adding Potassium Nitrate or Ammonium Acetate changes the community composition
Western Sierra Collegiate Academy
These are so cheap and easy to create, that it is frequently done in a classroom setting.
A local AP biology teacher, Beth Dixon started building these columns in her classroom last year.
This year, we are teaming up.
Field trip to Bodega to collect sediment samples that will be used to inoculate the columns under 5 different experimental conditions that Hannah and Cassie are currently defining.
The second challenge associated with citizen microbiology is data visualization.
Microbial ecologists have approximately 3 methods of visualizing microbial community data: the pie chart, the stacked bar chart, which is just a rectangular pie chart, and the PCA plot.
I’m picking on pie charts here, but the ”pie chart problem” is a proxy for a general problem with engaging data visualization.
I will explain later why the pie chart is problematic, but first I will show you two cit sci micro projects that are doing a good job engaging citizen scientists with visual representations of their microbial communities
The first is american gut. This crowd-sourced project allows anyone the opportunity to compare the microbes in their guts to those in the guts of thousands of other people in the US and elsewhere.
Here is what David Coil received after participating in American Gut. It’s on display in our lab. It includes a bar chart, comparing the phyla in their guts to various cohorts. And Michael Pollan. Every time I look at this, I think that Craig Venter must be kicking himself for not making HIS gut microbiome the one to whom all others are compared.
It also shows some PCA plots which don’t convey much information about the taxonomic composition of your sample, but does place it in a few different contexts.
The second project is one of the Your Wild Life projects run out of Rob Dunn’s lab at NSCU. They invited citizen scientists to compare the microbial inhabitants of their belly buttons to others
Participants in the Belly Button Biodiversity project are provided with a link that takes them to a page where they can interact with their results. They present an average pie chart, and then people can choose their belly buttons from a drop down menu. Mousing over the pieces of the pie allows the taxon name to pop up. They also provide users with a series of questions that they can answer with their data, which I think is key to engagement
For Project MERCCURI, we are planning to take advantage of a web-based interactive visualization tool developed by Holly Bik back when she used to be a postdoc in the Eisen lab.
However, despite what I consider to be the best case scenarios for sharing microbial community composition data with participants in these projects, I think we can do better.
I used to think that people hated pie charts the way they hate Comic Sans. Somewhat irrational, but coming from a design/aesthetics perspective.
But, actually, pie charts are a problem because the human brain is not good at estimating area. And, it is worse at estimating angles than lengths, so the stacked bar chart is an improvement upon the pie chart for that reason. However, when the number of chunks in a bar or pie chart increase, the value of the graphic to convey information about overall community composition takes a nose dive.
So, what is the solution? I’m sure there are many, because I’m not the only one dwelling on this problem, but I think this tricky problem requires experimentation with creative, alternative solutions, and I’m going to share an example of one of those with you now.
Given that human brains are not well-equipped to interpret pie charts, how can we present microbial community data in a form of which we can make sense? The solution to this problem lies in a region of the brain called the fusiform gyrus.
This region of the brain allows us to process a particular, very complex image in an instant, undergoing relatively little decomposition into component parts. Instead, they are encoded via a holistic or integrative mechanism, as a gestalt.
The human face is the result of tweaking hundreds (thousands?) of parameters. And yet, when we look at one, we know in an instant if we’re faced with friend or foe, if that face is happy or sad. We know if we’ve seen that face before, we even know if we’ve seen that face before, but something has changed since we last saw it. We can detect similarities between faces, we can detect asymmetries in faces.
What if we could build a face that represents a microbial community? How would we do that? Well, for a first stab at it, which is what I’ll present here, we could use the relative abundance of a particular microbe to dictate a value for a facial feature.
This particular human face was designed with this software that is used for 3D animation, like for video games and movies. The facial features are controlled by these sliders, and information from slider movement is written to a nice human readable text file. Each of 100s of parameters used to build these faces slide from a value of -1 to 1
For a simple example, I will vary 8 parameters on this face. The numerical value of each parameter ranges from -1 to 1, so I have scaled the relative abundance accordingly.
Here are the 8 features.
Now, first, I’m going to show you what this face will look like if we take each of these parameters to its extreme.
For a simple example, I will vary 8 parameters on this face. The numerical value of each parameter ranges from -1 to 1, so I have scaled the relative abundance accordingly.
Here are the 8 features.
Now, first, I’m going to show you what this face will look like if we take each of these parameters to its extreme.
So, what does this look like with real data? My test case is some 16S rDNA PCR data obtained from some experimental seagrass tanks. I’m going to show you three water samples and 3 sediment samples.
So, here are the 6 samples in the form of a bar chart. What can we glean from this?
I’m just going to point out 3 things for you to focus on.
There’s more variation in the bottom three than in the top three
The sediment samples contain a greater proportion of Deltaproteobacteria, relative to the seawater samples.
The seawater samples contain Thaumarchaeota, which the sediment samples do not.
How do these data translate to the human face?
So far we’ve been looking at the representation of only 8 taxa, just for illustration.
But real data often look like this. And, I think herein lies the real value of alternative methods of visualization that take better advantage of our innate capacity to recognize patterns.
Instead of presenting people with this
We can show them this. Picking out similar faces is quick and easy, even when we have no idea what makes them similar
Or, we could hone in on a particular feature, maybe you want to group all of the guys with this haircut.
And speaking of haircuts, altering the style and color of hair, while not changing the face itself, can make a dramatic difference in appearance. We can take advantage of this by changing the color or style of the hair, or the color and style of clothing to represent our metadata, allowing people to easily group microbial communities based on their similarity to each other, and independently accounting for the metadata.
So, imagine if in the future, David’s American Gut results come back looking like this.
And, if I haven’t already convinced you that faces are worth exploring as a data visualization tool, I will close with a few quotes to get you thinking more about their potential